is there still a prediction that can be made, or does it become an unfalsifiable mess?

I think that is debated, but molecular phylogenies are perhaps testable.

One of the pieces of evidence for evolution, claimed as a successful prediction of the “new synthesis”, has been the tree of life, in the sense that phylogenies derived from both genetic and morphological data are supposed to match each other.

In the case of a mangrove/DAG/Gordian knot of horizontal gene transfer, is there still a prediction that can be made, or does it become an unfalsifiable mess?

Note that this change of metaphor also requires changing the mapping from metaphor to reality. In Darwin’s tree, each node (or equivalently, each node’s parent branch) represents a species or clade. In the DAG, if each node represented a species, the graph would be cyclic, since species A can transfer genes to species B and vice versa. In order to have a DAG as you suggest, each node must represent one end of a gene-transfer event, i.e. we must have a new node (at least on the recipient side?) wherever a gene transfer occurs. It doesn’t appear that Dagan et al have constructed their drawing that way… the y axis only represents descent, and time by implication.

An interesting prediction of this model would be that a DAG *exists*, that can account for all the evident gene transfers, i.e. without going backward in time. Whether that’s a trivial condition to meet or not, I don’t know.

this tree bush mangrove thicket Gordian knot

Yeess… but if the most recognizable feature (that of tending to a single lateral transfer) is of the process, not of its outcome, it would IMHO be best if the new metaphor describes that instead.

Janne is then closer with his DAG description, but it is general as a metaphor.

As a process this reminds me of parachute canopy formation (formation involving a state change of the parachute, somewhat analogous to the lateral transfer). (And as a picture it reminds me of tree canopies mixing, keeping some connection to the earlier logic, as well as the earlier metaphor specifically.)

So the “canopy [formation] of life”, perhaps?

Are there any genes at all that have been confirmed to have jumped more than once?

“Tumor cells in Dog B, Dog C, Dog D, and Dog Z are more closely related to each other than those cells are to the dogs they respectively inhabit.”

Next, the scientists identified genes that are found in a tuft of branches, as well as to a single living species.

From context, I’m guessing it should read “…as well as in a single living species on a distant branch,” or something like that. If not, please explain.
thx

[Carl: You inferred rightly. I've tweaked the post. I hope that's clearer now.]

Horizontal gene transfer is advocated by Carl Woese. Wikipedia uses a diagram of a “Phylogenetic tree showing high rates of horizontal gene transfer between organisms.”

Now a serious question: Are there any similar estimates for viral transfer of DNA with eukaryotes? In your book you mention this is a rare sort of gene transfer. How rare is it?